1 Intro

This report provides some basic description of the peptide identificaiton from maxquant database search. The report is based on the peptide.txt, without defined experimental design/grouping information Users can use this to quickly check the overal quality of the experiment

2 Take home figures

  • Number of contaminant: 80

  • Number of reversed: 178

  • Number of qualified peptides: 19705

  • Number of quailfied peptide without intensity information(0 intensities): 481

  • Number of experiment: 1

  • All experiments: Intensity

3 Peptide Charge States

4 Peptide Length

5 Peptide Score distribution

6 Peptide Intensity distribution

Columns starting with “LFQ_intensity_” will be selected if exist (meaning LFQ option was checked for label free quantification, which is deliberately processed by Maxquant already), otherwise Intensity_ columns will be used instead for protein experession.

6.1 Sparisty

6.2 Sparsity cummulative curve

Figure shows how many peptides have more than N presence, which helps to set the presence cutoff

6.3 Intensity disitribution acrross samples/experiments

Heatmap of Presence 100

7 Download the neat table

The table is clean peptides expression table, with reversed and contaminant removed. The values are the LFQ(with label free quantification turned on) or raw protein intensity from Maxquant output. You can download/export and start from this table for downstream analysis using the (i)Metalab faminly apps.